αH(i,i+1) NOEs in helical peptide, can this be present continuously...

[Vivekanandan Subramanian]

Hi,

I have observed some interesting NOEs for my peptide (5 kDa) in my 2D NOESY spectrum recorded at 900 MHz. I see NOEs that forms an α-helical pattern between 12-24 residues and N&C-terminus of my peptide is unstructured and does not have any secondary structure. The interesting part is, apart from seeing helical NOE patterns, such as αN(i,i+3)and αβ(i,i+3) for the residues between 12 & 24, I see in the alpha proton chemical shift regions of my 2D NOESY spectrum, a continuous αH(i,i+1) NOEs for the residues where I have helical secondary structural region (12-24 aa). That is, I see NOE patterns like 12Hα -13Hα, 13Hα to 14Hα, 14Hα-15Hα, 15Hα to 16Hα, 17Hα-18Hα, 19Hα to 20 Hα and so on until 24th residue. In general, I have never seen in any literature reported this type of NOE patterns for the α-helical peptide. The mixing time that I used for my NOE is 300 ms. Did any of you have observed this type of Hα(i)-Hα(i+1) NOEs for α-helical regions of peptide? I would appreciate your answers and thanks a lot.
- Vivek

[krishnarjuna]

Hi,

If you are observing alpha-alpha NOEs continuously it must be beta sheet structure. In alpha helix you should observe continuous NH-NH NOEs. If both are present then your molecule must be existing in two conformations.

cheers, krishna.

[poah]

how do the ha to ha noe's compare to the hn to hn Noe's for the same residues.

300ms is pretty long for a 5kda peptide - it wouldn't be surprising to see spin diffusion errors.